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Detailed information for vg1014467198:

Variant ID: vg1014467198 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14467198
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATTTAGTCAACTATTATTAGATATATAGTATCCATAACCTTGACAAAATTTATTATGAAAATATATTCAGTTATTACTATATTTATCTAGAAACTTAG[T/G]
CAAACTTAAAACAATTTGACTTTGATCAAAGTCAAAATGTCTTATAACATAAAACGGAGAGAGTATAAAAGGAATATAGAAAATATGATACAAATACAAT

Reverse complement sequence

ATTGTATTTGTATCATATTTTCTATATTCCTTTTATACTCTCTCCGTTTTATGTTATAAGACATTTTGACTTTGATCAAAGTCAAATTGTTTTAAGTTTG[A/C]
CTAAGTTTCTAGATAAATATAGTAATAACTGAATATATTTTCATAATAAATTTTGTCAAGGTTATGGATACTATATATCTAATAATAGTTGACTAAATCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.60% 11.50% 0.40% 0.53% NA
All Indica  2759 99.40% 0.40% 0.04% 0.11% NA
All Japonica  1512 64.90% 34.00% 1.12% 0.00% NA
Aus  269 92.60% 0.00% 0.00% 7.43% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.30% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.00% 0.38% NA
Temperate Japonica  767 95.60% 3.10% 1.30% 0.00% NA
Tropical Japonica  504 18.10% 81.00% 0.99% 0.00% NA
Japonica Intermediate  241 65.10% 34.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 20.00% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1014467198 T -> G LOC_Os10g27420.1 upstream_gene_variant ; 3755.0bp to feature; MODIFIER silent_mutation Average:27.4; most accessible tissue: Callus, score: 49.717 N N N N
vg1014467198 T -> G LOC_Os10g27430.1 upstream_gene_variant ; 1831.0bp to feature; MODIFIER silent_mutation Average:27.4; most accessible tissue: Callus, score: 49.717 N N N N
vg1014467198 T -> G LOC_Os10g27440.1 downstream_gene_variant ; 2929.0bp to feature; MODIFIER silent_mutation Average:27.4; most accessible tissue: Callus, score: 49.717 N N N N
vg1014467198 T -> G LOC_Os10g27420-LOC_Os10g27430 intergenic_region ; MODIFIER silent_mutation Average:27.4; most accessible tissue: Callus, score: 49.717 N N N N
vg1014467198 T -> DEL N N silent_mutation Average:27.4; most accessible tissue: Callus, score: 49.717 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014467198 NA 1.17E-10 mr1055 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 1.86E-09 mr1336 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 5.90E-09 mr1539 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 7.66E-07 mr1543 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.77E-08 mr1642 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 1.97E-08 mr1668 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 9.42E-29 mr1699 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 9.21E-06 mr1742 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.49E-12 mr1864 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 7.47E-10 mr1905 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 5.08E-11 mr1022_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.31E-17 mr1023_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 1.59E-15 mr1079_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 5.64E-14 mr1132_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 9.91E-16 mr1178_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.21E-08 mr1261_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 7.59E-13 mr1390_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.71E-10 mr1398_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 7.84E-07 mr1398_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 3.78E-15 mr1489_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 6.97E-08 mr1668_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 2.52E-28 mr1699_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 1.17E-12 mr1742_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 1.05E-06 mr1860_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1014467198 NA 5.33E-09 mr1905_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251